7JRP

Plant Mitochondrial complex SC III2+IV from Vigna radiata


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Atomic structures of respiratory complex III 2 , complex IV, and supercomplex III 2 -IV from vascular plants.

Maldonado, M.Guo, F.Letts, J.A.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.62047
  • Primary Citation of Related Structures:  
    7JRG, 7JRO, 7JRP

  • PubMed Abstract: 

    Mitochondrial complex III (CIII 2 ) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III 2 +IV), play key roles in respiration. However, structures of these plant complexes remain unknown. We present atomic models of CIII 2 , CIV, and SC III 2 +IV from Vigna radiata determined by single-particle cryoEM. The structures reveal plant-specific differences in the MPP domain of CIII 2 and define the subunit composition of CIV. Conformational heterogeneity analysis of CIII 2 revealed long-range, coordinated movements across the complex, as well as the motion of CIII 2 's iron-sulfur head domain. The CIV structure suggests that, in plants, proton translocation does not occur via the H channel. The supercomplex interface differs significantly from that in yeast and bacteria in its interacting subunits, angle of approach and limited interactions in the mitochondrial matrix. These structures challenge long-standing assumptions about the plant complexes and generate new mechanistic hypotheses.


  • Organizational Affiliation

    Department of Molecular and Cellular Biology, University of California Davis, Davis, United States.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1A,
K [auth M]
527Vigna radiata var. radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3TWG4 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3TWG4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-MPPB,
L [auth N]
506Vigna radiata var. radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3VF71 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3VF71
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
COBC,
M [auth O]
393Vigna radiataMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
cytochrome c1-2, heme protein, mitochondrialD,
N [auth P]
306Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3W199 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3W199
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE,
O [auth Q]
271Vigna radiata var. radiataMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3TB49 (Vigna radiata var. radiata)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7F,
P [auth R]
122Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3U9J1 (Vigna radiata var. radiata)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
cytochrome b-c1 complex subunit 8G,
Q [auth S]
72Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3U9S5 (Vigna radiata var. radiata)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6H,
R [auth T]
69Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3VHC0 (Vigna radiata var. radiata)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
cytochrome b-c1 complex subunit 9I [auth J],
S [auth V]
72Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3TQD2 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3TQD2
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
QCR10J [auth K],
T [auth W]
81Vigna radiataMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
COX1U [auth a]527Vigna radiataMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2V [auth b]251Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3TZB2 (Vigna radiata var. radiata)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
COX3W [auth c]265Vigna radiataMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
COX4X [auth d]79Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3TNX9 (Vigna radiata var. radiata)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
cytochrome c oxidase subunit 5b-2, mitochondrialY [auth e]150Vigna radiata var. radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3U1E4 (Vigna radiata var. radiata)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
cytochrome c oxidase subunit 6a, mitochondrialZ [auth f]100Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3UMA0 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3UMA0
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
cytochrome c oxidase subunit 6b-1AA [auth g]181Vigna radiata var. radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3VV60 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3VV60
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5CBA [auth h]64Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3V319 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3V319
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
COX7aCA [auth i]67Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3TUX2 (Vigna radiata var. radiata)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
COX7cDA [auth j]96Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3V7C2 (Vigna radiata var. radiata)
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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GA [auth A]
GB [auth P]
HA [auth C]
IB [auth S]
PA [auth C]
GA [auth A],
GB [auth P],
HA [auth C],
IB [auth S],
PA [auth C],
QB [auth a],
RA [auth D],
VA [auth M],
YA [auth O]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
HEA
Query on HEA

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JB [auth a],
KB [auth a]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PC1
Query on PC1

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FA [auth A],
HB [auth S],
HC [auth i],
NB [auth a],
WA [auth M]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE
Query on 3PE

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AC [auth c]
BB [auth O]
BC [auth c]
CB [auth O]
CC [auth c]
AC [auth c],
BB [auth O],
BC [auth c],
CB [auth O],
CC [auth c],
DB [auth O],
DC [auth c],
EB [auth P],
EC [auth d],
GC [auth h],
JC [auth i],
KA [auth C],
LA [auth C],
MA [auth C],
NA [auth C],
OA [auth C],
OB [auth a],
PB [auth a],
RB [auth a],
SA [auth F],
SB [auth a],
TA [auth G],
TB [auth a],
UB [auth a],
WB [auth b],
XA [auth O],
XB [auth b],
YB [auth b],
ZB [auth c]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
HEC
Query on HEC

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FB [auth P],
QA [auth D]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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AB [auth O],
IA [auth C],
JA [auth C],
ZA [auth O]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
LYS
Query on LYS

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IC [auth i]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
CUA
Query on CUA

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VB [auth b]DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN
Query on ZN

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EA [auth A],
FC [auth e],
UA [auth M]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

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LB [auth a]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
MG
Query on MG

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MB [auth a]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references